The phenotype of many species of livestock, crops and pastures depends on the interaction between the genotype of the individual and the genotype of a symbiont. Important plants, including forage grasses, legumes, trees, shrubs, and vines are commonly found in association with endophytes including fungi, bacteria, viruses and microbes. Similarly, important animals, including cattle, sheep, pigs, goats, etc. have microbiomes present in their gut and rumen.
Both beneficial and detrimental horticultural, agronomic and veterinary properties result from such associations, including improved tolerance to water and nutrient stress and resistance to insect pests.
For example, ryegrass plants can show improved drought tolerance and persistency if a fungal endophyte of the correct genotype colonises the plant. Similarly, in grasses, insect resistance may be provided by specific metabolites produced by the endophyte, in particular loline alkaloids and peramine. Other metabolites produced by the fungal endophyte, for example lolitrems and ergot alkaloids, may be toxic to grazing animals and reduce herbivore feeding.
Considerable variation is known to exist in the metabolite profile of symbionts. For example, fungal endophyte strains that lack either or both of the animal toxins have been introduced into commercial ryegrass varieties.
Bacterial microbiomes also influence plant performance (e.g. in ryegrass, wheat).
In animals, the microorganisms present in the gut are responsible for digestion of an animal's feed. Ruminants host an extremely large and complex array of microrgansisms in their rumen, and it is this microbial community which allow them to convert low quality forage into high quality protein and lipids for human consumption in the form of meat and milk. During this process methane, a potent greenhouse gas is produced. Rumen microbes-bovine symbiota may be important, for example, in improving feed conversion efficiency and reducing methane production. In ruminants, successful digestion of poor quality feed may depend on having a particular rumen microbiome profile. If it could be demonstrated that regions of the host genome are associated with differences in rumen microbial profile, then this could be exploited to breed cattle with lower methane emissions and improved feed conversion efficiency.
Molecular genetic markers such as simple sequence repeat (SSR) markers have been developed as diagnostic tests to distinguish between symbiont taxa and detect genetic variation within taxa. For example, the markers may be used to discriminate symbiont strains with different toxin profiles.
However, there remains a need for methods of identifying, isolating and/or characterising organisms which exhibit symbiotic behaviour with symbionts. Difficulties in artificially breeding of these symbiota limit their usefulness. For example, many of the novel endophytes known to be beneficial to pasture-based agriculture exhibit low inoculation frequencies and are less stable in elite germplasm.
Moreover, in traditional breeding techniques, for example in forage grasses such as perennial ryegrass and tall fescue, grass varieties are bred using classic cross-breeding techniques and grass genotypes are selected for their superior characteristics, after monitoring their performance over a period of multiple years. The selected grass genotypes that form the experimental variety are then inoculated with a single endophyte and the resulting grass-endophyte associations are evaluated for any favourable characteristics such as insect resistance. The individual experimental synthetic varieties deploying a single endophyte in them are then evaluated for agronomic performance and resulting animal performance by grazing animals over a period of years. This evaluation process may reveal that the single endophyte being deployed in the different experimental synthetic varieties may not show vegetative and/or intergenerational stability in some of these varieties or the desired alkaloid profile conferred by the single endophyte may vary between different synthetic varieties failing to confer appropriate levels of insect resistance or causing animal toxicoses. It would be a significant development in the art if this time-consuming process could be accelerated or otherwise improved.
It is accordingly an object of the present invention to overcome, or at least alleviate, one or more of the difficulties or deficiencies associated with the prior art.